rs6099847

Variant names:

• chr20-57926923-T-C
• rs6099847

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.286 in 151,840 control chromosomes in the GnomAD database, including 7,144 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43359 AN: 151722 Hom.: 7111 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.286 AC: 43437 AN: 151840 Hom.: 7144 Cov.: 32 AF XY: 0.284 AC XY: 21099 AN XY: 74198

African (AFR) AF: 0.466 AC: 19269 AN: 41320

American (AMR) AF: 0.217 AC: 3315 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3468

East Asian (EAS) AF: 0.155 AC: 799 AN: 5166

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4816

European-Finnish (FIN) AF: 0.220 AC: 2325 AN: 10546

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14857 AN: 67930

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.243 Hom.: 16083

Bravo AF: 0.293

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.79
PhyloP100		1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6099847; hg19: chr20-56501979;